Relative codon adaptation index, a sensitive measure of codon usage bias. (Q40886512)

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:20535230%20AND%20SRC:MED&resulttype=core&format=json

5 February 2020

title

Relative codon adaptation index, a sensitive measure of codon usage bias (English)

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5 February 2020

1 reference

Soohyun Lee

1

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5 February 2020

Seyeon Weon

series ordinal

2

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5 February 2020

Sooncheol Lee

series ordinal

3

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5 February 2020

Changwon Kang

series ordinal

4

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5 February 2020

publication date

5 May 2010

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Evolutionary Bioinformatics

5 February 2020

published in

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5 February 2020

volume

6

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5 February 2020

page(s)

47-55

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Transcriptome and proteome exploration to model translation efficiency and protein stability in Lactococcus lactis

5 February 2020

cites work

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2880845

Selection for minimization of translational frameshifting errors as a factor in the evolution of codon usage

24 September 2017

1 reference

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Comparison of correspondence analysis methods for synonymous codon usage in bacteria

24 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2880845

CAIcal: a combined set of tools to assess codon usage adaptation

24 September 2017

1 reference

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SCUMBLE: a method for systematic and accurate detection of codon usage bias by maximum likelihood estimation

24 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2880845

Genome landscapes and bacteriophage codon usage

24 September 2017

1 reference

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The CAI Analyser Package: inferring gene expressivity from raw genomic data

24 September 2017

1 reference

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Absolute protein expression profiling estimates the relative contributions of transcriptional and translational regulation.

24 September 2017

1 reference

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The action of selection on codon bias in the human genome is related to frequency, complexity, and chronology of amino acids

24 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2880845

Variation in the strength of selected codon usage bias among bacteria

24 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2880845

Correlation of codon bias measures with mRNA levels: analysis of transcriptome data from Escherichia coli

24 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2880845

On the methodological weakness of 'the effective number of codons': a reply to Marashi and Najafabadi

24 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2880845

Intragenic spatial patterns of codon usage bias in prokaryotic and eukaryotic genomes

24 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2880845

The 'effective number of codons' revisited

24 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2880845

On the genetic basis of variation and heterogeneity of DNA base composition

24 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2880845

Use and misuse of correspondence analysis in codon usage studies

24 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2880845

Synonymous codon usage in bacteria

24 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2880845

Thermophilic bacteria strictly obey Szybalski's transcription direction rule and politely purine-load RNAs with both adenine and guanine

24 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2880845

A sampling of the yeast proteome

24 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2880845

Expression pattern and, surprisingly, gene length shape codon usage in Caenorhabditis, Drosophila, and Arabidopsis.

24 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2880845

Correlation between protein and mRNA abundance in yeast

24 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2880845

Base composition skews, replication orientation, and gene orientation in 12 prokaryote genomes

24 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2880845

Evolution of codon usage bias in Drosophila

24 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2880845

Maximizing transcription efficiency causes codon usage bias

24 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2880845

Asymmetric substitution patterns in the two DNA strands of bacteria

24 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2880845

Effects of rare codon clusters on high-level expression of heterologous proteins in Escherichia coli

24 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2880845

Codon usage in bacteria: correlation with gene expressivity

24 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2880845

Correlation between the abundance of Escherichia coli transfer RNAs and the occurrence of the respective codons in its protein genes: A proposal for a synonymous codon choice that is optimal for the E. coli translational system

24 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2880845

Codon usage and tRNA content in unicellular and multicellular organisms

24 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2880845

The codon Adaptation Index--a measure of directional synonymous codon usage bias, and its potential applications

24 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2880845

The 'effective number of codons' used in a gene

24 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2880845

Evolution of codon usage patterns: the extent and nature of divergence between Candida albicans and Saccharomyces cerevisiae

24 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2880845

Evolutionary patterns of codon usage in the chloroplast gene rbcL.

24 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2880845

Accounting for background nucleotide composition when measuring codon usage bias.

19 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2880845

DNA sequences from the str operon of Escherichia coli.

19 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2880845

Use of modified BL21(DE3) Escherichia coli cells for high-level expression of recombinant peanut allergens affected by poor codon usage

19 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2880845

A theoretical analysis of codon adaptation index of the Boophilus microplus bm86 gene directed to the optimization of a DNA vaccine

4 November 2018

1 reference

12 December 2020

Evolution of Gene Overlaps: Relative Reading Frame Bias in Prokaryotic Two-Component System Genes

1 reference

12 December 2020

Codon usage determines translation rate in Escherichia coli

1 reference

12 December 2020

Comparison of synonymous codon distribution patterns of bacteriophage and host genomes

1 reference

12 December 2020

The correlation of protein hydropathy with the base composition of coding sequences

1 reference

12 December 2020

Identifiers

DOI

10.4137/EBO.S4608

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:20535230%20AND%20SRC:MED&resulttype=core&format=json

5 February 2020

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:20535230%20AND%20SRC:MED&resulttype=core&format=json

5 February 2020

1 reference